The present invention relates to a method for producing a fermentation product from a sugar hydrolysate. The method comprises fermenting the sugar hydrolysate in a fermentation system with yeast to produce a fermentation broth comprising a fermentation product; introducing acid and an oxidant, such as chlorine dioxide, to the fermentation system so as to expose microbial contaminants in the fermentation system at one or more stages to chlorine dioxide and a pH of less than 3.0; and recovering the fermentation product. In one example of the invention, a yeast slurry obtained from a yeast recycle step is treated with acid and the oxidant.